


The Dreaming City

by camshaft22



Category: Stargate Atlantis
Genre: Action/Adventure, Big Bang, Gen
Language: English
Status: Completed
Published: 2011-06-03
Updated: 2011-06-03
Packaged: 2017-10-20 02:41:06
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 9,989
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/207905
Author URL: https://archiveofourown.org/users/camshaft22/pseuds/camshaft22
Summary: <blockquote class="userstuff">
              <p>John discovers a new enemy and something new about the city</p>
            </blockquote>





	The Dreaming City

Sometimes the city seemed too quiet altogether for him, like the silence that they had found on the day when they came here, had grown, stretched over all of them and slowly spread its heavy blanket over the sleeping city. Sleeping...from where John Sheppard stood the city was not sleeping, her bright spires shone out into the dawn of another early morning. On the outside the city seemed awake, bright and sparkling, but the silence remained, only interrupted by the perpetual song of the waves. Sheppard stifled a yawn, it was entirely too early for his run with the big guy, but what did it help? He turned around to leave the balcony and go inside the tower, but the door opened and slammed shut again entirely too fast. Frowning he stepped back and repeated the action. This time the door opened and he passed, only to see it stuck open beside him. The lights on the corridor ahead of him were flickering, reminding him of a broken neon-display. “Damn...” Sheppard tapped his earmike. “CIC this is Sheppard, we have power fluctuations in the North Spire,”

“We have power fluctuations everywhere, Sheppard. What’s it doing?” Rodney answered the radio as he worked furiously.

“It is lights flickering, Rodney,” Sheppard did not need to imagine that Rodney was probably hacking away at the CIC’s main systems. “and the doors are stuck... scratch that, the lights just failed.” He stood in complete darkness, except for the minimal light that came in through the still open door. But the grey dawn outside did not lend much light to the hallway.

“You’ve got to be kidding me... It’s reading as full power, which means we can’t trust the computers. You’d better get down here. Tell me if you see anything on your way,” Rodney said waspishly.

“On my way,” Sheppard sprinted down the dark hallway, luckily he knew this part of the city very well. He reached the transported doors which suddenly opened for him, but instead of the familiar menu of transports in the city on the map, he saw a totally foreign set of controls labeled in ancient. “Rodney, this is Sheppard, transporters have power but their controls have switched” He looked at them, some of the symbols were pretty similar to the ones in command center. “Let’s try this...”

“What? Ok, I’ll add it to the list of malfunctions,” he said with a tired sigh. “Did you make it?”

“No, I am a green cauliflower now,” Sheppard griped back. “It beamed me to the west bridge, instead of CIC, I better try to make it on foot.” He was already crossing the bridge as he spoke, he would have to make it up nearly the entire central spire, and all the more he hurried.

“Ha, Ha, Colonel. I don’t have time for your so-called wit today. When you get here, I want to try something.”

“If you’re out of trying on your own....” Sheppard stopped; he had reached the tower, finding two of their men stuck behind a door where the emergency shielding had powered up. “Sir, controls don’t respond!”

Sheppard recognized the man, Dr. Sikorski, he had had the gene therapy and the controls should respond to him even if the city was acting up on the protocols. “I will try from my side,” he said. It was a lucky break; the controls released the shield allowing the two scientists to escape their trap. Sheppard hurried on, reaching the dark stairwell. “Rodney, systems are acting up all over the city, we might have people trapped inside their quarters or other rooms. Have you heard from Mr. Woolsey?”

“No. Not yet, but I have been trying to stave off the utter meltdown of the entire city. He might be trapped somewhere since that’s what seems to happening. Try your radio,” Rodney told him.

Keeping up the rapid pace up the stairs, Sheppard tapped the earmike again. “Mr. Woolsey, this is Sheppard, do you copy?” He was vastly relieved to hear Richard Woolsey’s voice over the radio.

“I can hear you, Colonel, where are you?”

“I am on my way to CIC, we are experiencing malfunctions all over the city,” Sheppard reported. “Are you alright?”

“I am trapped in my... I am trapped but in no danger, Colonel. Head up to CIC and assist Dr. McKay with fixing the problem.” John heard a noise in the background and suddenly had the wild guess that Mr. Woolsey might be stuck in his bathroom. “On my way, Sheppard out.” he replied quickly.

“John. Where are you?” Rodney asked as Czech cursing filled the background.

“Nine levels below you, Rodney,” John had duck as a window splintered before him, splattering glass all over the floor. A tall figure appeared in the broken frame, climbing in. “None of the doors would open.” was the gruff report her heard. “Ronon just joined me; he too says that the doors stopped working.” John frowned. “I had no troubles with them. We should be with you soon.”

“Did you just-? He BROKE the DOOR?!” Rodney yelled.

“He climbed the tower and smashed a window, Rodney, calm down!” John snapped, with Ronon in tow they considerably picked up the pace, the big guy having his own definition of hurry. They reached the next landing, the door was down, but once John reached it, it open. “This is getting weirder and weirder,” Sheppard commented, as they made it up the last flights of stairs and reached the command center.

Rodney moved his mouth a few times then growled, getting back to work as his fingers flew over the keyboard. Teyla entered the room and caught Rodney’s attention.

“What is it that you need me to do?” Teyla asked.

“Watch that monitor and everytime it flashes red, press these keys. That will restart it and hopefully warn us in time.”

John was panting hard as he reached the final door, the run up the long stairwell had left him short of breath, and neither the flickering lights nor other weird malfunctions did help his mood much. Again the door refused Ronon but let Sheppard pass. They entered CIC, secretly Sheppard was glad to see Teyla was alright. “Rodney, what’s our status? Apart from the obvious...”

“We’re floating. Other than that, everything, down to the smallest thing is either shorting out or working half the time. I’ve got Teyla making sure we’re staying afloat. But I need you to get into the chair. It keeps shorting out on me.”

“Alright, the chair room is in a different tower and several levels down,” Sheppard replied. “Ronon stay here, for some reasons the doors don’t work for you.” The tall man shrugged, indicating he had no clue why the doors only worked for Sheppard.

Rodney frowned slightly. “Teyla, you and Ronon help Radek,” he told them. “Lead the way, Sheppard.”

Sheppard turned back to the door that slid open for them and allowed them back into the halls. A fine watery spray touched his face. He scowled. “The cleaning cycle must have activated, I did not ask for a shower from Momma.”

“She must think your Cologne stinks,” Rodney told him as he carefully shielded his padd.

“Har har,” John griped back. “Maybe she decided that you need a hair wash,” he fell into a jog as they made their way towards the stairs. “We better take the long way, I’ve got no clue what got into the transporters.”

“Great. So... Ok, what did the transports do exactly?” Rodney asked, trying to get a better feel for the problem.

“The menu was different, not a map but a long list of locations, I think, all in Ancient of course. And it teleported me not to another transporter but to some other point in the city,” John told him, as they hurried down the long stairwell. “Could it be that there is a second transport system that got activated by accident?” After six years in this city he should be used to knowing that they did not know how it worked and that surprises could jump them at any time.

“It would make since to have some sort of secondary, but the very nature of them makes a redundant system asinine. No. It’s got to be another setting or something. Maybe the default... Why is this only working for you, anyway?”

“I don’t know,” John rubbed his hand against his forehead. “it just does... like back in Antarctica, I sat down and it came alive.” Like in their first weeks here, until they got the settings adjusted. But it was still different, because it excluded the people with the artificial gene.

“Weird. But something might be there. Let me think on it,” Rodney told him. “Tell me if you feel anything strange.”

“Feel anything...?” John knew what Rodney meant. He had sometimes sensed things from the Ancient tech before. “Let’s wait what I can say when we reach the chair.”

The chair room opened before them and it looked eerie because the only thing that had some light was the chair itself, everything else was huddled in darkness.

Rodney chilled upon entering the room. “Let me check the control panel...”

“Alright,” John walked up to the chair, when he stood before it, the familiar blue light lit up brightly. “Whoa... I think we try this the hard way,” he said, sitting down.

Rodney looked up at it as it shone brightly, swearing under this breath. “Let’s... Let’s start this slow. Picture where you are in the galaxy.”

John relaxed, feeling the familiar touch of Atlantis on his mind. He focused and a huge holograph sprang alive, showing the galaxy and their position, with a number of systems marked with complex entries. “That’s... new,” he said softly. It was beautiful.

Rodney looked at it in awe. “It.. It’s more defined... more... I don’t know. Can you access the systems at all?”

“I think so...” John exhaled, smiling. The galaxy vanished and a complex schematic of blue lines appeared above them. Some of the lines were silvery to green, but most were blue, forming patterns and knots. “That’s... I think that’s the main schematics,” John said softly. “I... I can try to access systems directly. What should I be looking for?”

“Security protocols. This might be a security glitch,” Rodney told him, amazed by what he was seeing.

John closed his eyes focusing on the security protocols, causing several new holographs to appear. “It seems there is... some kind of a breach,” he said to Rodney. “if this was a PC I would simply say reboot, to get the firewall straightened out.”

“Yes... But luckily you’re not in charge of maintenance. Can you elaborate? What sort of breach?”

“Like a security protocol that was meant to keep certain functions locked away because they were disruptive has been deactivated through something and now we have conflicting functions on the systems.” John knew the words fell short of the complexities of the system he saw.

Rodney frowned, furrowing his brow. “We need to reset the entire system... but I don’t know that we possibly can...”

“I think it is possible,” John said, his eyes following rapidly something he alone could see. “It will be somewhat of a restart, but it should set the systems back on track. At least that’s what this protocol is meant for...”

Rodney tried looking where John was staring. “Do it. Let’s see if that works.”

John tried to make Atlantis show the things he was seeing in a hologram, and it did actually, thus Rodney could follow the process as the cities systems were powered down and then rebooted, with resets. The process was straining, requiring John to stay focused on the system all the time. His head was pounding, but the longer it went the more came online correctly.

Rodney radioed Teyla as John used his Gene to reactivate systems. “John needs something to drink... possibly some juice or some fruit...”

“I will go myself. Unless you need me for something else?” Teyla told him.

“No... Sheppard took care of that... he looks like he’s going to pass out or something.”

“Very well, Rodney. I will bring you something.”

“Thanks.”

“I am not going to pass out, Rodney!” John snarked up, his voice strained with exhaustion. He felt like all his energy was pumped into keeping going with the system. “I am not some weird damsel in distress,” he griped while another part of the city rebooted and came online the way it had been.

“Quit being a baby. You’re doing things to yourself that shouldn’t be possible. So eat something so maybe you don’t faint.”

“Who is a baby?” John pressed out the words, his body shaking with exhaustion. He accepted the bottle that Teyla had been bringing down, wanting to take a sip, but instead he slipped off the chair, falling unconscious. The chair’s lights went out, but the city was back to normal.

“I need a Medical Team to the Chair Room!” Rodney called out.

 

John was running, the corridor stretched before him like a long-winded path, he looked back over his shoulder in haste, and the lights were burning and flaring, how long had he been running? The lights grew brighter, silvery lights falling into the halls. John kept going, he did not know where. But he had to go back to the core. Had the path always been so long? Or had he forgotten?

No sleep, only waking without consciousness...

Whispered a voice, echoing through the endless hallways. John tried to stop and listen but he was too fast, the voice drifted past him like a whisper in the winds. He tried to turn around but behind him were the blaring lights, the burning light. Behind were they, making the lights burn out, he could not go back. He must go on, he must reach the core.

Always walking, always calling.

John woke panting, blinking into the lights of the infirmary. It must be in the dead of night and he had been dreaming.

One of the nurses walked over to where he was waking up. “Colonel. Glad to see you awake. Do you need anything to drink? Are you feeling hungry?” she asked, starting to check his readings.

John blinked. “What happened?” He had been in the chair because of some malfunction. He rubbed his head. “Never mind... I am fine. Just a little tired.” He pushed himself up. “The malfunctions? Have they stopped?”

“Most of them, yes. But we’re having a few issues. But if we have a natural geneholder, we can usually just bypass whatever it’s trying to do. Dr. McKay was forced to get some sleep... but I’m told he’s got an idea of how to fix it...”

“Good,” John nodded, “I will see him in the morning, so we can get this fixed up.”

The next morning found John hungry and looking forward to breakfast outside the infirmary. He was meeting up with Teyla at the entrance of the mess hall.

Laughter made John turn around. A girl - a small girl in a white dress - stood in the middle of the hallway. “Catch me!” she grinned at him, running away.

Blinking Sheppard stared at the empty hallway. “Where is she?”

Teyla frowned and looked around. “John?” she asked, scanning the area.

“That... that little girl, she was right there...” John rubbed his eyes. “I must be half asleep, if I start seeing stuff. Don’t tell Rodney, will you?” He looked pleadingly at Teyla. Rodney would poke John about having visions mercilessly.

“I will not tell him... but if this continues, please, tell me or someone else?” Teyla asked him.

“I am sure it is nothing,” John said, waiving it off. He was tired, and had dreamt too much weird stuff the night before. “Let’s eat something and find Rodney, to get Atlantis fixed.” John already noticed that some doors were opening and closing on their own. Time to get this worked out.

“It would definitely be for the best,” Teyla told him with a warm smile. They got their trays, seeing Ronon already waiting for them.

“Sheppard, you okay?” Ronon asked, as they sat down.

“I’m good, where is Rodney?” John asked, hungrily attacking his breakfast.

Ronon shrugged. “In his lab,” he guessed. “There was some problem with the transporters again.”

John put aside his fork. “Damn, we need to get this get in check. I heard Rodney had some idea?” He was interrupted by a spray of water coming from the ceiling; the self-cleaning mechanisms had gotten active again. John scowled. “So much for breakfast. Let’s find Rodney.”

“Good idea,” Teyla said, eating her toast and rising to her feet so they could hurry down to where Rodney was. “It is a good thing Torren is with his Father. I don’t think it would be good to have him here during this.”

“You are right,” John replied. He was not quite sure what Teyla’s and Kanaan’s relationship was, or... ah, he just knew he did not know. Which was weird enough. “I am glad he is safe until we figure out what is going here.” They hurried out of the messhall and towards the labs to find Rodney. When they entered the hallway leading down to Rodney’s lab John frowned. Those lights... they were like the ones in his dream, too yellow. Not silver. He shook his head, what a crap. Lights were lights. “Rodney, tell me you have a fix for this?”

“If I had a fix for this, it would’ve already been fixed, don’t you think?” Rodney told them as he looked at them. “But I am glad that you’re here. I need you to go to the chair.”

“Let me guess, finding out what is wrong?” John replied. “Let’s go.” When they came out of Rodney’s lab, the little girl was standing in the middle of the corridor. She clapped her hands and shook back her dark brown locks. “Catch me, John...” she called before skipping away, vanishing into thin air. John had reached for her, but grasped nothing. “Wait...!”

Teyla put a hand on John’s arm to get his attention. “John?”

The touch of Teyla’s hand brought John back to notice his surroundings. “She was there again,” he said, still looking at the spot. “a little girl, seven, maybe eight years old, she has long brown hair and she wears one of those fancy white dresses...” he realized how weird that sounded. “Forget it, let’s get to the chair.”

“John... Do you believe it is like when the Whales were trying to contact us?” Teyla pressed, not letting him just dismisses this.

John frowned, remembering the incident. “If it was something like that, why don’t you see her? You were the most sensitive to them.”

“Teyla’s right,” Ronon stated, his arms crossed in front of his chest. “Maybe something is trying to tell you something.”

“Maybe and maybe I just have some whack on the head from my time in the chair yesterday,” John replied.

Teyla frowned at him. “If this continues, please tell us. For now, we should get you to the Chair.”

“Agreed,” John pushed the picture out of his mind and they proceeded down to the chair room. When they walked in and John came close the chair lit up by itself. “Whoa... that’s new,” John said. He had not even touched the chair yet.

Rodney looked at his read out and gasped. “Oh no. No... No, no, no!” he said, taking off at a run as he tapped his radio. “Sheppard, stop, stop now!”

Sheppard had tapped his radio to tell Rodney the chair was active, but there was no answer. “The radios must be affected,” he told Teyla, as he sat down in the chair. The moment he touched it, he could feel, sense the systems far stronger than before. Leaning back, he made himself relax, ease into the stream of information flowing into his mind. A circle of holograms became alight around him and above him, but in his mind John could nearly see the city from a different perspective, like he was soaring high above, seeing it all at once.

Teyla heard Rodney shouting as he ran towards them. “Stop him! Stop him now!” he yelled as he sprinted past them into the Chair room.

A shield had flared up around the chair and John felt invisible energy bands securing him in the seat, making it impossible for him to move. He breathed slowly, focusing on the system to get more of an input on what was wrong. “Oh crap...” His eyes widened, unaware that the others saw the holograms and not the same systems he saw. “McKay! Have your guys check the ZPM stat! There is a power build up in the ZPM chamber...” he shouted, while zooming in on the systems.

“Ronon, I need you to run down there, the radios aren’t working!” Rodney ordered him as he worked on it remotely.

Teyla looked at John as glowing lines snaked up his arms. “Rodney!”

Rodney nodded. “I saw that it was doing something weird... I tried to get here before he started. We’re just going to have to hope for the best...”

John’s eyes were following the glowing lines, the complex diagraph that was the city’s main power system. “I have to reroute power, to prevent critical levels...” it was not easy to reroute power and it caused a lot of other systems to go haywire or simply loose energy but that way he could reroute the immense power output away from the ZPM before it could explode. “Teyla... tell Rodney that the power must come from somewhere else in the city, I am trying to locate and shut the source..:”

Teyla hesitated and looked at Rodney. “Rodney is here, Colonel. He is aware,” she told him.

“Just keep doing what you’re doing, Sheppard,” he told him, feeling a bit panicked as he watched the glowing lines snake up John’s body.

John did only hear the voice from far away, his mind drawn closer into the system. “This is incredible...” it was part of a complex system that he could see where the power was generated and... had they ever even seen those systems before? Most likely not. “I think I can reroute the power, but I can’t shut down the source,” he said after few moments. “But I can make sure the power does not negatively impact on the other systems.”

“Ok. Ok, do what’s needed. Can you get out of the chair?” Rodney asked him.

“Not right now,” John replied, sounding absently. “The shield system seems to be meant to secure the pilot under combat conditions, no idea why it suddenly went active. But there is a whole bunch of stuff that we never saw here before.”

“Like what?” Rodney asked, trying to monitor him.

“I don’t know what all of them are, Rodney!” John snapped, trying to focus. “But some seem to be industrial systems somewhere in the city’s underbelly and... something big, where the power is coming from. No clue where it is, it’s... it’s hard to understand even when it projects into your brain.”

“I’m trying to get you to tell me what you think it is!” Rodney snapped at him.

“John, try clearing your mind. You’re being peppered with things, right? Try to calm your mind and control it.” Teyla told him.

“This system... it’s huge, from here it looks like everything is flowing there, and coming back, power, data... but it is complicated, like layers and layers of programming, of numbers...” John’s eyes zoned out and his breathing became labored. All of sudden the chair shot forward, going inactive, releasing him. He panted, trying to steady himself.

Teyla immediately went to his side, her eyes wide as she noticed that the glowing lines hadn’t ceased. “Rodney...”

“Oh Damnit...” Rodney swore, seeing the still glowing lines embedded in his skin. He had no idea how to deal with this...

John twisted his head, to see what Teyla was staring at. “I didn’t say I’d get another tattoo...” he griped, surprised.

“What in the hell is that?” Rodney asked.

John touched the blue lines glowing in his skin; they were beautiful, weird as that sounded. Under his fingers they felt cool, but somehow alive. “I don’t know,” he admitted. “It doesn’t feel bad, though. More... like Atlantis itself...” he paused, from the moment he had first sat in that chair in Antarctica he had felt a kind of familiarity with it. Dr. Weir had simply said he was a natural but there was something else to it. Something he had a hard time explaining. And this just felt like another extension of it.

Ronon came into the room, having returned. “Zelenka says ZPM power is at normal levels again;” he reported. Seeing the blue lines on Sheppard’s skin he added: “Maybe Doctor Keller should check you out.”

“Definitely. Let Jennifer figure this... whatever it is, out.” Rodney told John worriedly.

“I am fine,” John got to his feet, actually finding he could, and he wouldn’t show them that he was a bit wobbly.

“No, you aren’t,” Ronon gave Sheppard a light push, that landed him squarely on his butt. “You can hardly stand.” The tall man grabbed Sheppard’s hand, pulling him and supporting him to bring him to Dr. Keller.

Dr. Keller felt like saying something about the usual suspects when she saw Ronon half dragging, half carrying Col. Sheppard into the infirmary. Usually this happened right after sparring incidents of various sorts. And if Sheppard did not protest loudly about being semi-carried he had to be bad. “Put him down here,” she told Ronon, her eyes widening when she saw the blue lines on the Colonel’s skin. “Rodney, what happened?”

“I asked him to use the Chair and there was an odd power spike before he got into it. I couldn’t stop him in time and the chair did that to him.”

“Alright...” Jennifer was not quite sure what to say. They knew not enough of the way the chair interfaced with the human physiology to make any judgment easy. She wished Dr. Beckett were here, he had been conducting the initial studies on the chair. Not wasting any more time, Jennifer had Sheppard moved to the scanner, to begin an analysis.

It had taken Dr. Keller two hours to conduct her preliminary checks; luckily Sheppard had fallen asleep and not griped at her all the time. When she came out, aside of Rodney and the team, Mr. Woolsey was waiting as well. “How is he?” The Atlantis leader asked worried.

“He is exhausted,” Keller said. “The chair took again a lot out of him; we have him on IV to supply the basic needs of his body. There also is the huge strain these sessions have on the mind, so his sleep comes as no surprise.”

“What about these tattoos?” Woolsey asked. “What are they?”

Jennifer sighed. “That’s the tricky part; they interface with his vegetative nervous system. At first I believed they were a physical remainder of the interface with the chair, but the way they connect they would not allow of any conscious thought or information being transported,” She called up the scan results. “Then I noticed there... The cells around Colonel Sheppard’s nerve columns are regenerating much faster and better wherever they are touched by those lines. I think... I think the chair scanned Sheppard and recognized that his body could not sustain the strain, and then applied measures to support him.”

“So, what is this going to do to him? What are the permanent effects of this?” Rodney asked.

“As far as I can tell it mainly sustains him, helps his nerves to regenerate at a higher rate... I can only imagine the damage the initial input from the chair must have been causing, to need that kind of healing.” Dr. Keller said. “As far as I can tell it beneficial, Rodney. But what long-term effects it will have... we can only wait and see.”

“So, this is a kind of healing the system applied to prevent damage to Colonel Sheppard while he was in the chair?” Mr. Woolsey inquired.

“Yes,” Jennifer turned to the Atlantis leader. “The Ancients were very proficient with technologies that encompassed healing. It is well possible that they were aware of the dangers the chair could pose when used under such strain and created a kind of failsafe to prevent casualties.”

“So, he’s regenerating in a way...” Rodney said with a bit of awe.

“Essentially yes,” The lights of the infirmary flickered rapidly and some systems went offline. “From a purely selfish standpoint... he might be able to handle the chair better next time and maybe be able to fix the mess.”

“It’s not selfish. We need the city to work or we’ll all die,” Rodney told her. “Thanks, Jennifer... I’m going to see what I can do to stave off some of the damage...” he said, squeezing her hand gently before taking off.

The corridor before him seemed to draw on endlessly, John was racing down the hallway, behind him the lights changed, and they were raging. He took a shark turn and down yet another hall, those corridors never ended, like one winding line going on and on, walking in circles forever.

Always calling, always waking....

The voice, he had heard it before. Somehow he knew that voice.

Never dreaming, only waking without waking... calling into the emptiness...

John turned around, following the voice, he did not care that it brought him back to them. He would fight, but he needed to hear that voice. He needed her.

Suddenly he stood in the chair room, but it was a different room, in a different place, several people were around working on the systems, a man was sitting in the chair, his dark hair sweat-damp, blue lights encasing his body. “Another wave is coming in... give me all you can...” his voice was strained and somehow John knew he was flying the city, and fighting a battle...

Somehow he knew this man would die, die in the chair...

Always calling, always waking... searching...

The voice whispered.

Panting John woke, his body shaking like a leaf. He exhaled. It only had been a dream. He rubbed his temples, spotting the faintly glowing patterns on his arm. He smiled. They felt good, warm, like a friendly hand on his arm.

Rodney was working on something as the City continued to log him out. He growled, wanting to shake the screen.

Dr. Keller saw that Colonel Sheppard was awake. “How are you feeling?” She asked.

“I am good,” John replied, swinging his legs off the bed. “But from the state of the lights, the city isn’t.”

“No, it’s getting worse.” Jennifer confirmed. “But you...”

“.. Shouldn’t be hanging around here, while I am needed.” John finished her sentence. He grabbed his BDU’s and a few minutes later he was headed towards CIC.

Rodney looked up and frowned. “Sheppard? What are you doing here?” he asked.

“Helping you out,” John said, approaching the console. He put his hand on it and it powered up correctly, logging them in. “there you go, that’s better.... oh crap...” his eyes went to the screen that showed the long range sensor readings. “Don’t tell me those are ships we have incoming.”

“What did you- What?” Rodney said looking at the long range sensors. “We’re screwed!”

“No, not yet,” John replied grimly, tapping his ear mike. It did not work. Blast it! He stepped to another console, he did not know how he knew but another system came alive, giving him citywide. “May i have your attention, this is Colonel Sheppard, we have several unknown ships inbound on our location. Military personnel report to your combat stations, all non-essential personnel remain in your quarters.” Hastily John hurried towards the other consoles, switching them on, so his people could work. The shield came up-

Rodney looked at him and got to work, knowing what to do. But he couldn’t keep from looking at John, checking on him as he merely touched things and made them work.

John did not notice Rodney’s looking, nor the stared of the others. “Chuck, any communications from them?”

“No, Sir... they do not answer our hails.” Chuck was still shocked that his console suddenly worked again without hiccups.

“Alright, time to open the dance,” if Sheppard was aware he sounded cocky was questionable. “Chuck, I’ve transferred secondary fire controls to your console, fire one single drone across the bow of the first ship as a warning shot. Rodney, any ID on our new unfriendlies?”

“It’s definitely not a hive ship... and it’s a ship that the computers don’t recognize. Have we made new enemies?” Rodney asked.

“Doesn’t seem like new friends,” John replied, he raised his hand, the wave brought up another screen, a holograph showing their tacticals. “Chuck? Any reaction?”

Chuck wondered if this could get any crazier, the new menus popping up at his console, being actually the secondary fire controls, the primary controls were still in the chair. “No, they definitely don’t speak ‘warning shot’,” The first three ships opened fire, the city was shaking when their shots hit the shield.

John steadied himself against a console. “Maybe they will understand a drone barrage,” he growled.

The two other ships made their flyby, new hits coming down on the shields.

“Sir?” Lorne asked, having used his own connection with the system to activate the city comms. “We have visuals on the ships. It’s nothing like we’ve ever seen before...”

“And they are not very friendly,” John could see them in the holograph swing by for another pass. “The shields are holding, but we need to get them out of our sky. Take fire control, when they come back, we fire the drones at them.” They would need to fluctuate the shield for the drones to pass it, but they could handle that.

“On it, Sir,” Evan told him, taking over the fire control. As they swung around, he fired, trying not to think about that he was doing it with his mind.

The drones did hardly more than grazing the enemy ship’s shields, while their incoming fire rocked the city. “Shields are holding,” John was grateful that shields could draw on some of their extra power. Something good out of a pile of trouble. But the aiming the drones with the secondary controls must be for Lorne like fighting in the quicksand. The secondaries were not designed to work as precisely as the chair. “Lorne, we need a man down in the chair for firing the drones,” Sheppard said. “But I can’t leave here, or Atlantis will log out our people again.” His fingers were hammering on one console, creating a workaround for several systems.

“I’m running now, Sir,” Evan told him, running down to where the Chair was. He threw himself into it and gasped as he connected fully into the city.

John was glad Lorne got to the chair, thus he could concentrate his efforts on keeping the defense running and keeping their people in the right systems. At least he had managed to pull up most of the secondary controls up to CIC and log them into Chucks, Rodney’s and his own console. The ships came in with another pass stacking up the bombardment.

Rodney got to work, firing and trying to get analysis on what they were facing.

Evan let himself delve into the systems as he concentrated on firing and trying to find a weak spot. “Sheppard,” Evan said, trying to get his attention. “I think I found their weak spot...”

“Good! We have the shield fluctuations lj-cut up, so the drones should pass quickly,” John informed him. They could not afford any direct hits, the city was too vulnerable. “Fire when ready,” John knew Lorne would find the best spot.

Evan fired, hitting them and targeting the spot he found earlier.

Rodney looked as the screen. “We’re receiving a transmission,” he said, running it through the translation software they had.

“Let’s hear it,” John said. “Lorne, hold your fire, our friends want to chat.”

Rodney pulled up the feed. “Surrender or die, Alteran filth! We will have our revenge!” the man growled at them as Lorne paused.

John touched a key on the console. “Atlantis will never surrender, turn back or be destroyed,” he said, not realizing he had been speaking Ancient. “Lorne - fire at will.”

Lorne started firing at them.

Rodney rose to his feet. “John! You’re speaking Ancient!”

“Did I?” John rubbed his forehead. “It is... it is just the language that is in the system, I guess it must have dumped some translation into my brain, or simply put the appropriate knowledge into my mind.” He could not explain it.

Onscreen they could see two of their ships getting hit by the drones, going up in fire. “Whohoo.... Lorne! Two hits! Well done - 2 down, 3 more to go...” John heard the alerts from some systems and turned to his console, preparing another set of workarounds to keep things together in spite of the malfunctions.

Evan concentrated and fired more before his vision went blurry and he fainted in a heap.

Rodney frowned deeply. “Once this is finished... We’re going to run some tests,” he told him, stubbornly.

Outside, the drones did surgical strikes, making two of the ships explode.

Two ships went up in a flare, and the fire control came back from the chair. “Lorne!” John called out, but there was no response over the city communications. “Medical team to the chair room!” John ordered. The third ship had swung around, their weapons hit the shield, weakening it just enough to allow one torpedo to pass the barrier, the explosion shook the city, damage reports were coming in. John was about to wonder if he should go to the chair to finish the job, when suddenly all the consoles flared alive, systems working by themselves, without any input from them, as the consoles locked against their interference.

They could see the long range communications come alive. Flee, Brakhian, before death takes you. This city will be a light in the darkness until your darkness dies. An eerie voice announced over the system towards the enemy ship.

A vibration ran through the floor, a shivering all too familiar. “Oh no no no.... the star drive can’t be active...”

“It’s doing it by itself. I can’t get anything to respond!” Rodney reported as he struggled with it, trying to get it to work and not do this anymore.

John touched the console, but could sense a definite block on the system. The city was rising from the surface, several drones keeping the enemy ship at bay. But Atlantis was definitely flying. “I’ll head down to the chair, it’s the only place where I can do anything.” John said, sprinting off, taking the shortest possible way towards the chairroom. Through some windows he passed he could see they were in space and shortly after they were jumping to hyperspace. Damn... this was not good. Not good at all!

When he reached the chairroom, he felt like walking into a Deja vu - a figure, or something closely akin to it, sitting in the chair. The figure was pale, like an over bright holograph, but John still recognized the man he had seen in the dream, the one he dreamed would die in the chair. “Your friend needs healers...” he heard the voice, before the shield around the chair went up.

Evan opened his eyes feeling like he was hung over. He scanned the half-lit Infirmary and opened his mouth to ask a question as Teyla leaned in.

“Shhh. Don’t move, Major. Allow me to get you something to drink and alert Dr. Keller,” Teyla told him gently.

“She is right here,” Jennifer pointed out, putting the finishing touches on the bandage on Sheppard’s right wrist where an electrical burn had singed him badly. She turned to check on Lorne. “You were very lucky, Major - the chair left you badly exhausted.”

Teyla glanced at Dr. Keller and nodded, leaving them to speak.

Evan looked at her and nodded. “I definitely feel it. What happened? We were attacked, what happened after that?” he pressed, knowing something was wrong.

Sheppard rose from his place, wincing and ignoring Keller’s pointed look. “We got a hit through the shields and... something went weird,” He said to Lorne. “The stardrive fired up by itself. When I came to the chairroom you were unconscious and... we were flying guided by something not caused by us.” He did not mention the specter he had seen. “By now we’re out of hyperspace, stranded. Most of the cities systems are locked, we can’t get access.”

“And he got a nasty burn when he tried to circumvent some systems to get access to the chair room again.” Keller added. “It is like the city itself is fighting us.”

“The City is fighting us? I don’t understand... Why would it now?” Evan asked.

“That’s what we have been trying to understand,” Teyla told him. “There is no reason for this.”

Evan looked at Sheppard. “Did the city... I don’t know, Sir... Did it connect to you in a different way?”

John met Evan’s eyes. Had he heard the apparition speak? He shook his head. “Okay, this will sound crazy...”

“More crazy than your usual?” Keller quipped.

“Yes.” John wondered what they would say. “When I found Lorne in the chairroom, I saw an apparition again. Not the little girl, another one. A man - like a ghost, sitting in the chair. He had the shields around the chair up and.... he said to me that Lorne needed medical attention.” He looked away, knowing the next was just the weirdest. “It’s not the first time I’ve seen him. I saw him in a dream before... saw him in the chair, and in that dream I knew he would die.”

“Was he tall, bearded and looked like he belonged in a roman battlefield?” Evan asked. “I’ve seen him in my dreams lately... and I meant... Atlantis, the city... When I was in the chair, it felt like I was more than just me...”

“Tall, dark, short beard... warrior type, yes that’s him.” John confirmed surprised. “So... you’ve seen him as well.” He looked at Teyla. “I am sorry, six years ago, when you wished to speak that prayer for the spirits of the ancestors I thought it was nuts. Maybe you were right after all. Something is haunting the place.”

Teyla looked at him, surprised. “It is not too late. Perhaps it would help us?”

“Given the current situation, I think more that we need to talk to them, find out what they want and why they took control of the city.” John replied. “Something made them come out of hiding... something triggered all this. First the malfunctions, then the dreams... and these...” he raised his arms where the blue lines shone under his skin. “We need answers, and I have no clue where to start.”

Evan looked startled and immediately lifted his arms to check, unable to mask the slight relief when he didn’t show signs of the blue lines.

Teyla frowned slightly. “Did the Ancestors not make redundancies? Perhaps these visions and dreams are a program within the city’s mainframe to help you undo whatever is making the city attack us.”

“Teyla is right,” Jennifer said. “The city might be trying to show you what is wrong.”

John looked at both women. “You think these corridors I am running through in my dreams that they lead where the problem is?”

“Couldn’t hurt to turn our attentions towards these areas, Sir,” Evan said, starting to get up so he could shower and re-dress.

“Okay,” John said. “Lorne - I need you to head up to CIC and take command. Most of the populace is locked in their sections; most of them are safe and need to be calmed. Rodney is trying to find workarounds but without access to anything he’s not standing much chance. Teyla.... you are with me... I might need your help trying to track those dreams.”

“Yes, Sir,” Evan told him, putting off his shower and looking for his earpiece. He put it back in and hurried off to the CIC.

Teyla nodded. “Where do the dreams begin?”

John closed his eyes trying to recall where the dreams started. “It always begins with me running...” he said recalling the pictures. “running down a long hallway... it is curved, I can’t see much ahead, but there is a huge window on my left side and through the rain I can see the North Pier.” he stopped, his eyes snapping open. “I think it’s the bridge linking those spires just off North Pier.”

“Then we should hurry there. Are those sections sealed off?” Teyla asked as they left the Infirmary.

“I don’t think so, the main lockdown seems to be in the central spire,” John said, already hurrying off. It was easier than he thought to find a way that brought them there. Stopping at the bridge John looked around. “This is the place Teyla, but the lights... they are different, in front of me they are golden, warm - behind me they are white, cold. And it is that light that I am running from, and them but ... for the life of me I don’t know what that means-”

 

“Perhaps there is meaning there. You said Them, John... The enemy? Could they already be here?” Teyla coaxed, trying to get him to open up.

“I don’t know,” John said. “there is this voice, whispering. No sleep, only waking without consciousness...” He began walking in the direction he had been running in the dream. “and I keep running, wondering if the path always has been so long.”

Teyla followed, having her weapon ready. “We should follow the path you left yourself.”

John began to walk quicker, remembering the path he had been running, following a twisted way through the city. It was corridors they hardly had ever entered before. When they came down a stairwell he stopped. “I... I think there is something, Teyla.” he said. “in that dream I wonder if the path always was so long and then... I think that I must reach the core. Whatever that is. But maybe... maybe that’s the place we need to find.”

“Perhaps Atlantis is leading you to this,” Teyla said as they looked around. “We may need to repair something and it was telling you.”

“Maybe,” John ran his hand through his hair. “but... why the fear... there is something I am running from in the dream. And the man... the man I see in the chair,” he suddenly stopped. “Teyla - the dream, the man he is in the chair or a chair at least, but it’s not in the chair room we know.” He picked up the pace again, sliding down a ladder, and turning left, following the track of where he had been in the dreams.

Teyla had no answer to John’s concerns as they went deeper into the unexplored city, their only roadmap, John’s dreams.

John felt like he was in the dream again, running along that path towards the core. Part of him knew he was not, but the eerie feeling grew stronger the further they went. Eventually they reached a transport that brought them up again, depositing them on a balcony high above the city. A glass door slid open, letting them into a room. The room itself was huge, reaching down at least twenty levels, catwalks connecting it with a complex construct in the middle - like one huge machine filling most of that tower. A control chair standing right on the platform where they had come in.

Teyla was breathless, seeing the vast inter-working of the city like this. She never imagined such a thing... “Perhaps we should get Rodney.”

John looked around. “Good idea,” I agreed.

Teyla retreated with urgency, knowing Rodney should be here for this. Her thoughts drifted for a brief moment towards Torren and Ronon, knowing that her son was safe with him. She hurried, going to where Rodney had camped out in the CIC.

“Teyla? What’s going on?”

“We have found something that Rodney needs to take a look at. Immediately,” Teyla told them, seeing how Rodney was about to protest.

“Oh, alright,” Rodney groused. “Is this about what’s causing this?”

“We believe so,” Teyla said, silently urging him to hurry.

Rodney saw the look she was giving him and got to his feet. “Lorne, if anything beeps, don’t touch it or anything.”

“Ok, McKay. Go and figure this out!” Evan told them.

Teyla started heading towards the room.

John stood in the silent spire, the core. He knew this was important, this was the very heart of Atlantis... the heart as it should be. But something was wrong. Something was stunted... there had been a reason for the dreams, and for the fear. “You couldn’t tell me more, can you?” he asked into the silence. “Whoever you are....” He knew he was talking to a ghost he had seen die in a dream. It was crazy.

“I died to protect this city, will you do the same?”

John whirled around, suddenly face to face with the same man he had seen before. He wore the black uniform he remembered. How he managed to appear was beyond John. “How... what is happening here?”

“Why don’t you ask her herself?” Was the cryptic answer.

John bit back a snappy answer. Since when had he come to expect a straight answer from anyone ancient? He turned towards the chair. With one like these his journey had begun years ago, and no matter what had happened, John would never regret that fortunate accident in Antarctica. But this... this was bigger. He knew it was something about this city that would change. And about himself.

He noticed that the ghostly appearance had the same blue patterns, only more intricate. “If you are ascended you are not supposed to interfere, ya know?”

“I am not.”

“Not ascended? That’s a new one.” John sat down in the chair, it light up, and at the same moment the core came alive again, golden lights flaring up warmly. And he saw....

Rodney’s eyes widened as he felt the touch of something go up his spine. He started running, making even Teyla hard pressed to keep up as his adrenaline fueled him. Rodney entered the room as blue lines snaked up John’s arms and body, each connecting in some unknown way as the pattern spread over his body.

John’s eyes lost their empty expression and focused on them. “Rodney, Teyla...” his voice was low, he had to remember to speak out loud. “I can get us out of this, just give me some time.”  
“What are you doing?” Rodney asked, alarmed, wondering if something had taken over his friend and was using him as a puppet.

Teyla put a hand on Rodney’s shoulder, trying to urge for calm as she watched John warily.

John exhaled sharply, his connection to the systems got easier as another blue pattern appeared on both of his temples. “Yes... that’s better. The Ancients really screwed this one up...” He said.

“Name something they didn’t. So what’s going on? You’re apart of the city now?” Rodney asked, putting the pieces together.

“That’s part of it,” John replied. “I guess Lorne should have the basic imprint as well... he too had the affinity.” He sat up straight, without the chair going inactive, it was easy now that he did not need it any more. “When this city was built, Rodney - the Ancient Scientists Janus and some other very smart people, gave her a new kind of core - a computer system like none before had ever been build. Technical details are way above any of our heads, but bottom line is - it was self-learning, developing, it had something like intuitive self-improvement systems. And eventually the city developed a mind of her own, a consciousness. Which was fine in the beginning. It was fine for a long time in fact. Only after the war, and the plague and after building the device of Dakara...” John shook his head, unable to translate the time line. “A new council rose, some people rose to the council who felt that many things had gone too far. They were... moralists, hardliners, their legislation ended a lot of research and... they decided that the sentient part of the city was going too far. They wanted to remove the core but that’s impossible, the city can’t work all her complex systems without it... so they devised a kind of firewall to block out her conscious mind. That’s why she was calling out to us. Always walking, always waking without consciousness. She had been stunted, lobotomized.” John smiled, a smile meant for the vast mind he knew with them. “but she only slept, and when we rigged the systems to allow our Earth tech, we eroded the firewall, until she could come out. But it was not easy, the access was sporadic and unstable.”

“So... The City is sentient... and now what?” Rodney asked, the possibilities and implications rushing through his mind at lightning speeds. “You’re still in the system...” he said, voicing his astonishment.

“Yes, the chairs are crude tools,” John replied. “the imprint serves to sustain the body as well as allow direct access to the system. It can have some side effects, as Lucien showed... Lu, you still here?”

“I did tell you to not call me that,” the man said, as he became visible to them.

“I could call you Lucy, you know?” John quipped, unable to not tease him.

“The man from your dream,” Teyla said, looking at him. “It is our pleasure to welcome you back.”

Lucien inclined his head towards Teyla. John smiled, leave it to Teyla to be diplomatic and respectful, she had a gift to make someone feel welcome at once. “Lucien was in the chair, flying the city, during a fight - back in the Milky Way, the very same war that ended in the plague that befell the Alterans. Lucien died and his mind fused with the city’s core. Apparently that could happen with me as well.”

“It is a side-effect of the imprint, your mind gets so close to the core, that it is possible that your mind will remain inside the network when your body expires.” Lucien explained. “It is not an absolute, though. I held on to closely trying to keep control of the systems when my body gave out.”

“So, it’s risky, just like everything else in the Pegasus Galaxy. But do you know what this means? We have someone, two people, who know what every little thing does! This is the best thing that’s ever happened to me. We can fix everything!”

Teyla gave Rodney a look and then bowed her head just slightly, apologizing for Rodney. “What do you know of the enemy that attacked us?”

John exchanged an amused look with Lucien. “Don’t mind Rodney, and if he grates on your nerves too much - replicate some lemon for him.” He got serious again on Teyla’s question. “I don’t know them, but Lucien, I think you do?”

“I do. They are the Contempari, that’s what we called them. The Plague bringers. We encountered them a long time ago in our home galaxy, and later again when they attacked the Milky Way. Some of them followed us here, but left off when they saw the galaxy was mainly uninhabited. The council believed they had gone -”

John rolled his eyes. “Of course, they believed their problem had gone away. Damn it, Lucien - how could such morons ever rise to power?”

“Perhaps now is not the time for such questions. How can we fight these invaders, Lucien?” Teyla asked, trying to keep them all on track.

“I shook the last one off when we jumped,” Lucien said. “so we have some time before they find us again. That’s why I brought us here - the asteroid belt outside has all the raw materials the city needs to affect repairs. And with the core unlocked, we can bring the city back to her full potential.”

“He means once the city is back to her old form, we will kick their butts.” John replied.

“We should get started on getting people without the Gene and with the artificial gene free... we’re going to need their help to do this,” Rodney told them.

“I am on that part,” John said. “the firewall protecting the main spire is tricky to get rid of, give me a minute, okay?” He waved his hands and a projection, showing some programming code appeared before him. “Lucien... can you reset the access for the people with the artificial gene? They will need access to the systems.”

“Done, John. I lowered the recognition pattern to pick up on genes of that insignificant strength, it will do until they can get a boost.”

John grinned. “Before they can get a boost Mr. Woolsey will get a shock.... the IOA hates surprises like that. But at least we can tell them it’s under control.”

Rodney scowled, not liking the comment about insignificant strength but stayed quiet.

 

Mr. Woolsey had hurried towards the spire, the moment his quarters finally unlocked and he got informed by Dr. McKay where to go. He had to admit, what he found inside the spire made him think mostly of Dr. Weir, she once had told the IOA that she never knew what to expect or find inside the city of the Ancients. And this... this was not the quiet Atlantis he had gotten used to. John Sheppard was still in the chair, the blue pattern on his skin growing, interweaving deeper with his body, the ghostly appearance beside him unnervingly quiet.

“Colonel, the lines on your body...”

“Are the Ancient version of a cyber-implant,” Dr. McKay interjected sounding his usual annoyed self. “they connect to the nervous system and spread throughout the body, allowing for interfacing on various levels, sustaining the body at the same time. They practically reach everywhere...” he looked Sheppard. “... don’t they?”

“Rodney!” Sheppard growled. “None of your business.”

“And our attackers...”

“An ancient enemy of the Ancients, the enemy who drove them from the Milky Way.” Again Rodney replied, clearly getting tired of repeating information.

“But what now?”

“Now, we prepare to fight.” Sheppard told him, rising from the chair, continuing the work without it. “Nothing has changed, and all has changed but still is the same.”

Seeing Sheppard take the lead, Teyla and Rodney fall in, Mr. Woolsey again thought of Dr. Weir. How often had she held back, guiding without directly leading? Had she been swept away at times? How would she have handled this? The IOA official in him insisted that the AI was not to be trusted, the man who had served in Atlantis for the past year and half knew it was the find of a lifetime. And there was a new enemy out there, an old enemy of the Ancients. More history, more dangers, and more to discover. Sheppard was right - what was new?

“I will return to the command center, Colonel,” Woolsey replied after a moment of silence. “If the city has to fight, we need the populace prepared.”

John looked up, like surprised. “Thank you,” he said, he did not need to elaborate on it, his meaning was clear without saying so. An enemy was out there, and they just had come across another piece of the grand legacy that Atlantis was, and it was only their trust in each other that would carry them through.

The End


End file.
